Table 1

Summary of the 10 human TPH1 SNPs genotyped in this studya

SNP name (Genomic localization)b

Position in the gene

SNP IDc

PCR primers and short-extension probee


5'flankingSNP1 (T-1721G)

5' flanking region

SNP000574351

F: 5'-ctgttcttttggtgtcctc-3'

R:5'-gctcctggcacttaacata-3'

P: 5'-taatttctttcatgagtattttatagtt

5'flankingSNP2 (A-1067G)

5' flanking region

SNP000574353

F: 5'-ctgttcttttggtgtcctc-3'

R: 5'-gctcctggcacttaacata-3'

P: 5'-ttttttgctgagtatggatgtactttaaagctcagga

5'flankingSNP3 (G-347T)

5' flanking region

SNP000574354

F: 5'-cgataataggcgttatcttg-3'

R: 5'-ctcaatctctgcgtgtatct-3'

P: 5'-tcaggactgggctattaaatagcccagaagcacagaga

in1SNP1 (T3804A)

Intron 1 (exon 1c)

rs623580

F: 5'-taattatcctccctccaagt-3'

R: 5'-cttacccattcaattaccac-3'

P: 5'-agagtatgggcgacgttgtccta

in2SNP1 (G7465A)

Intron 2

rs684302

F: 5'-tgctcttatatgtcttttcaagt-3'

R: 5'-gagagatggagcaaaacac-3'

P: 5'-ttaaataaaatacctgtatgtcttcttccatca

in3SNP1 (A12517C)

Intron 3

rs211105

F: 5'-tcaggaaaacagaagggta-3'

R: 5'-ggtaaattgccctatttctaa-3'

P: 5'-aggtggcaaagacaaatgatttctaagatcttttccatcggc

in6SNP1 (C18626G)

Intron 6

rs2237907

F: 5'-gggaagaaattatgtaagtgg-3'

R: 5'-gaaatgttccatatctgtgc-3'

P: 5'-ttgtaatgcacacaaaactgaaagctgatctcttagggtctggagc

in7SNP1 (A20004C)d

Intron 7

rs1800532

CF: 5'-acccacctacactttcctc-3'

CR: 5'-taattgacaacctattaggttc-3'

AR: 5'-agcacatgtgaagcatttag-3'

AF: 5'-cctatgctcagaatagcagctct-3'

3'UTRSNP1 (C27224T)

3' UTR

rs2108977

F: 5'-cacttgaatatcacagtccatc-3'

R: 5'-gcttacagtagatttccttgc-3'

P: 5'-tacatttgatggtaaatagatgctagctaatct

3'UTRSNP2 (A27237G)

3' UTR

New

F: 5'-cacttgaatatcacagtccatc-3'

R: 5'-gcttacagtagatttccttgc-3'

P: 5'-aactataaatcagataatcaata


a. in7SNP1 was genotyped using ARMS, while the other SNPs were genotyped using MSBE.

b. Genomic localizations of SNPs are given in bp relative to the transcription start site (position 0).

c. The ID for 5'flankingSNP1, 5'flankingSNP2, and 5'flankingSNP3 are from HGVbase http://hgvbase.cgb.ki.se/ webcite. The ID for in1SNP1, in2SNP1, in3SNP1, in6SNP1, in7SNP1, 3'UTRSNP1, and 3'UTRSNP2 are from dbSNP http://www.ncbi.nlm.nih.gov/SNP/ webcite.

d. The A20004C is known as intron7 A218C polymorphism.

e. All PCR reactions were performed at the same annealing temperature (53°C). F: forward primer, R: reverse primer, P: short extension probe.

Lai et al. BMC Medical Genetics 2005 6:14   doi:10.1186/1471-2350-6-14

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